长雄野生稻有利基因的发掘与利用

人类将普通野生稻驯化为亚洲栽培稻,其农艺性状如株高、落粒性、穗型等发生了重要变化,产量也大幅提高,但许多优良性状如抗逆性等却丢失。长雄野生稻与亚洲栽培稻同属AA基因组,蕴藏了许多生物胁迫和非生物胁迫的抗性基因,被认为是亚洲栽培稻遗传改良的潜在基因库。本文总结了长雄野生稻生物及非生物胁迫抗性、地下茎性状以及其他潜在应用价值性状,包括白叶枯抗性、抗旱性、耐热性、自交不亲和性、氮高效利用以及高产等有利性状。基于长雄野生稻地下茎性状开展多年生稻育种实践的应用研究,对长雄野生稻进行从头驯化的策略进行了探讨,以期为长雄野生稻基础研究及栽培稻遗传改良提供理论参考。     

我国野生稻资源的抗病性鉴定与利用研究进展

野生稻广泛分布于亚洲、非洲、拉丁美洲和澳洲的77个国家,目前公认有21个野生种,我国有3个野生种。野生稻具有大量栽培稻目前缺乏的的优良特性(基因),成为栽培稻遗传改良的丰富基因源和重要的物质基础。我国是水稻生产大国,但白叶枯病、稻瘟病、纹枯病等各种病害一直严重影响着水稻生产。从我国野生稻挖掘和利用抗病材料(基因),是培育抗病品种的重要途径。本文综述了我国野生稻资源的抗病性鉴定与利用研究进展,提出了存在的问题和加强研究的建议。     

小粒野生稻优异基因的挖掘与利用研究进展

小粒野生稻拥有丰富的遗传多样性,含有大量的优异基因,是进行栽培稻遗传改良和基因组研究的宝贵资源。本文总结了国内外研究利用小粒野生稻种质取得的系列进展,主要包括:小粒野生稻优异性状的鉴定和遗传群体的构建,小粒野生稻有利基因的定位、克隆与育种利用,还对小粒野生稻优异基因利用的困难和应对策略进行了讨论。这些结果必将有利于进一步挖掘和利用小粒野生稻的有利基因。     

中国野生稻收集、鉴定和保存现状

本通过介绍我国野生稻种质资源的考察、收集、繁种、编目、鉴定、评价和保存、保护状况,论述了我国野生稻丰富的遗传多样性和种质资源研究成就,针对目前存在的突出问题,提出了我国野生稻种质资源研究目标和主要任务。     

中国野生稻资源考察、鉴定和保存概况

本综述了我国野生稻种质资源的考察收集、农艺性状鉴定、编目、繁种、入库保存等情况。到目前为止,我国收集了野生稻种资源近万份,编目7324份,种子入国家种质库长期保存5599份,种茎进国家野生稻圃长期保存8933份,显示出我国野生稻资源丰富的遗传多样性,并得到较完善的保存。介绍了鉴定选出的一批具有优良性状的种质资源。作还提出加强野生稻资源保护和研究的6点建议。     

彩色小麦基因发掘和种质资源育种利用北大核心CSCD

随着人类对彩色营养功能小麦需求越来越大,彩色小麦遗传研究越来越深入,彩色小麦品种越来越多,但我国彩色小麦种质资源家底不清。为了满足国内外对彩色小麦营养遗传育种方面的迅猛需求,本文综述了彩色小麦基因和种质资源育种利用进展,首先介绍了彩色小麦基因来源的种质资源,其次介绍了彩色小麦染色体组及系谱,第三是首次全面总结了我国彩色小麦育种和种质资源创新的进展。我国近24年来审定了61个彩色小麦品种,其中紫(黑)粒品种50个,蓝粒小麦品种10个,绿粒小麦品种1个,还育成了19个彩色小麦种质新资源,其中近4年是我国彩色小麦品种审定最多的年份。河南省、山东省、河北省、山西省是我国4大彩色小麦育种和产业化基地。彩色小麦品种大部分来源于彩色小麦和普通小麦杂交,彩色小麦基因主要来自于小麦与野生一粒小麦、野生二粒小麦、偃麦草、黑麦、赖草等远缘杂交。有48个彩色小麦品种籽粒蛋白质含量超过14%,4个彩色小麦品种籽粒蛋白质含量超过18%,4个彩色小麦品种面团稳定时间超过10 min。针对彩色小麦遗传育种和产业化存在的问题,建议作物种质资源保护与利用要遵循“有差异,就选择;能遗传,可定向;有价值,就保藏;需鉴定,要精准;扬其长,广利用”的基本原则。以上资料将为我国彩色小麦遗传育种研究提供大量有用信息和基因种质资源,推动我国彩色小麦遗传育种研究深入发展。     

试论野生稻高蛋白种质在水稻育种中的应用

本文探讨野生稻高蛋白种质在水稻育种中应用的必要性、意义和可行性,提出研究应用的发展重点;认为水稻品质育种应利用野生稻高蛋白种质,加强专用水稻育种和高蛋白种质分子学研究。     

普通野生稻中增产相关QTL的发掘

普通野生稻(Oryza Rufipogon)是重要的遗传资源,发掘其优良等位基因将对水稻遗传改良产生重要影响。文章从以珍汕97为轮回亲本,普通野生稻为供体的BC2F1群体中选择一个与珍汕97表型明显不同的单株BC2F1-15,经过连续自交获得回交重组自交系BC2F5群体。均匀分布于12条染色体的126个多态性SSR(Simplesequence repeats)标记基因型分析,发现BC2F1-15单株在30%的标记位点为杂合基因型;利用该群体共检测到4个抽穗期、3个株高、4个每穗颖花数、2个千粒重和1个单株产量QTL。在第7染色体RM481-RM2区间,检测到抽穗期、每穗颖花数和产量QTL,野生稻等位基因表现增效作用;其他3个每穗颖花数QTL位点,野生稻等位基因也均具有增效作用。结果表明野生稻携带有增产相关的等位基因,这些有利等位基因无疑是水稻遗传改良可资利用的新资源。     

有机大米产业化与野生稻种质利用

针对有机大米产量明显低于普通大米的问题,本文论述了有机大米产业化与野生稻优异种质利用的关系,分析了野生稻优异基因利用现状、目前存在的问题以及解决问题的途径。提出在有机水稻品种选育过程中,通过利用野生稻优异基因,提高有机水稻品种抗病虫性、抗逆性(耐寒、耐旱、耐贫瘠)和光合效率等特性,从而推动野生稻优异种质利用,提高企业经济效益,解决化学物质残留和污染等问题。     

中国野生稻遗传资源的保护及其在育种中的利用

我国有三种野生稻,即普通野生稻(Oryza rufipogon)、药用野生稻(O.officinalis)和瘤粒野生稻(O.meyeriana)。这三种野生稻均被列为国家二级保护植物(渐危种)。调查结果表明,野生稻由于其自然群落大量丧失而濒危,濒危程度为普通野生稻>药用野生稻>瘤粒野生稻。造成濒危的主要原因是人为的破坏活动。人类的经济活动导致了野生稻生境丧失、生境质量不断恶化、栖息地越来越少;人类的活动也导致了外来种的入侵。目前,对野生稻的保护措施主要有就地保护(原地保护或原位保护)和迁地保护(易地保护或异位保护)。易地保护包括以种子保存的种质厍、以种茎保存的种质圃和以器官培养物作为材料的超低温保存。野生稻具有许多优良特性,如特强的耐寒性、高的抗病虫性、优质蛋白质含量高、功能叶片耐衰老的特异性、特强的再生性、良好的繁茂性及生长优势等等,这些优良特性已被广泛用于水稻常规育种和杂交育种中,并取得了巨大的社会效益和经济效益。有关野生稻生物技术方面的研究,如花药培养、原生质培养、体细胞杂交和基因工程等方面已取得了较大的进展。野生稻将在水稻育种中发挥越来越重要的作用。     

Discovery of rice essential genes by characterizing a CRISPR‐edited mutation of closely related rice MAP kinase genes

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein 9 nuclease (Cas9) system depends on a guide RNA (gRNA) to specify its target. By efficiently co‐expressing multiple gRNAs that target different genomic sites, the polycistronic tRNA‐gRNA gene (PTG) strategy enables multiplex gene editing in the family of closely related mitogen‐activated protein kinase (MPK) genes in Oryza sativa (rice). In this study, we identified MPK1 and MPK6 (Arabidopsis AtMPK6 and AtMPK4 orthologs, respectively) as essential genes for rice development by finding the preservation of MPK functional alleles and normal phenotypes in CRISPR‐edited mutants. The true knock‐out mutants of MPK1 were severely dwarfed and sterile, and homozygous mpk1 seeds from heterozygous parents were defective in embryo development. By contrast, heterozygous mpk6 mutant plants completely failed to produce homozygous mpk6 seeds. In addition, the functional importance of specific MPK features could be evaluated by characterizing CRISPR‐induced allelic variation in the conserved kinase domain of MPK6. By simultaneously targeting between two and eight genomic sites in the closely related MPK genes, we demonstrated 45–86% frequency of biallelic mutations and the successful creation of single, double and quadruple gene mutants. Indels and fragment deletion were both stably inherited to the next generations, and transgene‐free mutants of rice MPK genes were readily obtained via genetic segregation, thereby eliminating any positional effects of transgene insertions. Taken together, our study reveals the essentiality of MPK1 and MPK6 in rice development, and enables the functional discovery of previously inaccessible genes or domains with phenotypes masked by lethality or redundancy.     

Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm

Key message

The association of natural genetic variations of salt-responsive candidate genes belonging to different gene families with salt-tolerance phenotype and their haplotype variation in different geographic regions.

Abstract

Soil salinity covers a large part of the arable land of the world and is a major factor for yield losses in salt-sensitive crops, such as rice. Different gene families that respond to salinity have been identified in rice, but limited success has been achieved in developing salt-tolerant cultivars. Therefore, 21 salt stress-responsive candidate genes belonging to different gene families were re-sequenced to analyse their genetic variation and association with salt tolerance. The average single nucleotide polymorphism (SNP) density was 16 SNPs per kbp amongst these genes. The identified nucleotide and haplotype diversity showed comparatively higher genetic variation in the transporter family genes. Linkage disequilibrium (LD) analysis showed significant associations of SNPs in BADH2, HsfC1B, MIPS1, MIPS2, MYB2, NHX1, NHX2, NHX3, P5CS1, P5CS2, PIP1, SIK1, SOS1, and SOS2 genes with the salt-tolerant phenotype. A combined analysis of SNPs in the 21 candidate genes and eight other HKT transporter genes produced two separate clusters of tolerant genotypes, carrying unique SNPs in the ion transporter and osmoticum-related genes. Haplotype network analysis showed all the major and few minor alleles distributed over distant geographic regions. Minor haplotypes may be recently evolved alleles which migrated to distant geographic regions and may represent recent expansion of Indian wild rice. The analysis of genetic variation in different gene families identified the relationship between adaptive variations and functional significance of the genes. Introgression of the identified alleles from wild relatives may enhance the salt tolerance and consequently rice production in the salinity-affected areas.

     

Evaluation of phosphorus starvation inducible genes relating to efficient phosphorus utilization in rice

Plants develop strategies to recycle phosphorus so that all organs receive adequate amounts of phosphorus, especially new growing organs. To evaluate the metabolic adaptation of rice plants under phosphorus deficient conditions, we selected several genes related to phosphorus utilization efficiency in the cell. Phosphoenolpyruvate carboxylase, triose phosphate translocator, phosphoenolpyruvate/phosphate translocator (PPT), pyruvate kinase, NAD dependent glyceraldehyde-3-phosphate dehydrogenase, and NADP dependent glyceraldehyde-3-phosphate dehydrogenase were selected because of their important roles in phosphorus utilization by the cell, and because they are part of the proposed bypass pathways by which the cells save phosphate. The most dramatic change was observed in the expression level of PPT (which transports phosphoenolpyruvate (PEP) from the cytosol into the chloroplast); thus we believe that PEP may play an important role in maintaining carbon metabolism under phosphate deficient conditions.     

Discovery of wild tetraploid sweetpotatoes

Specimens in the germplasm collection at the U.S. Vegetable Laboratory, United States Department of Agriculture (USDA) in Charleston, SC, were studied to examine phylogenetic relations of the tetraploid accessions inIpomoea sectionBatatas. This collection contains tetraploidsfrom a wide geographic range and most were tentatively identified by the collector asI. trifida. This study shows that corolla and sepal traits may be used to distinguish the tetraploidsfrom known specimens ofI. trifida (diploid) andI. batatas (hexaploid). All but one tetraploid accession examined (CH67.50) had corolla tubes and sepals shaped likeI. batatas and more closely resembled that species thanI. trifida. Use of corolla tube diameter allowed the hexaploidI. batatas and tetraploid accessions to be distinguished fromI. trifida because the corolla tubes were wider immediately above the calyx. Differences in sepal shape were quantified using the angle at the sepal apex. This angle was consistently obtuse in theI. batatas hexaploids and the tetraploids, but was acute in theI. trifida accessions. Due to similarities in sepal and corolla traits, these tetraploids should be reidentified as tetraploidI. batatas, a cytological race of the hexaploid I. batatas (the sweetpotato).     

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.     

Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing

High-throughput sequencing of pooled DNA was applied to polymorphism discovery in candidate genes involved in starch synthesis. This approach employed semi- to long-range PCR (LR-PCR) followed by next-generation sequencing technology. A total of 17 rice starch synthesis genes encoding seven classes of enzymes, including ADP-glucose pyrophosphorylase (AGPase), granule starch synthase (GBSS), soluble starch synthase (SS), starch branching enzyme (BE), starch debranching enzyme (DBE) and starch phosphorylase (SPHOL) and phosphate translocator (GPT1) from 233 genotypes were PCR amplified using semi- to long-range PCR. The amplification products were equimolarly pooled and sequenced using massively parallel sequencing technology (MPS). By detecting single nucleotide polymorphism (SNP)/Indels in both coding and noncoding areas of the genes, we identified genetic differences and characterized the SNP/Indel variation and distribution patterns among individual starch candidate genes. Approximately, 60.9 million reads were generated, of which 54.8 million (90%) mapped to the reference sequences. The average coverage rate ranged from 12,708 to 38,300 times for SSIIa and SSIIIb, respectively. SNPs and single/multiple-base Indels were analysed in a total assembled length of 116,403 bp. In total, 501 SNPs and 113 Indels were detected across the 17 starch-related loci. The ratio of synonymous to nonsynonymous SNPs (Ka/Ks) test indicated GBSSI and isoamylase 1 (ISA1) as the least diversified (most purified) and conservative genes as the studied populations have been through cycles of selection. This report demonstrates a useful strategy for screening germplasm by MPS to discover variants in a specific target group of genes.